Ion beam deposition (IBD) is a well-known technique for depositing material on a substrate. In a typical IBD process, an ion beam is directed at a target, producing a flux of particles toward a substrate. Thickness variations in the deposited layers are a common problem, as the flux may not be uniform over the entire substrate. Also, in cases where the material is being deposited on features that extend outwardly from the substrate, there may be undesirable or asymmetric variations in deposition caused by shadowing effects and the like. The substrate may be rotated or moved to produce greater uniformity, but there can still be problems. Beam shapers, sometimes referred to as shapers, flux regulators, or shaper masks, may also be used to promote the desired layer deposition. Unfortunately, such techniques may not entirely correct such deviations from the desired pattern of deposition.